Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_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: 4987688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 20
Found at i:553412 original size:17 final size:17
Alignment explanation
Indices: 553377--553430 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
553367 GGCATGTGAA
553377 AATAA-ATAATAATAAT
1 AATAATATAATAATAAT
* *
553393 AATAATATAATGATATT
1 AATAATATAATAATAAT
553410 AATAATATTAATAAATAAT
1 AATAATA-TAAT-AATAAT
553429 AA
1 AA
553431 AAAATAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 5 0.16
17 16 0.52
18 4 0.13
19 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATAATATAATAATAAT
Found at i:553889 original size:133 final size:133
Alignment explanation
Indices: 553646--554041 Score: 422
Period size: 133 Copynumber: 3.0 Consensus size: 133
553636 ATCGATGTAA
* * * * *
553646 ACTTGTTCCATTGTTACTCAGGAAAGATCAAATCTTGGAAACGAGGGATATGTTCCGCTTCTTCT
1 ACTTGTTCCACTGTTACTCAGGGAAGATCAAATCTT-GAAAAGATGGATATGTTCCGCTTTTTCT
* * *
553711 TGAGGGAAAATCAGATCTGGGGACATTTATTCATTCCACTGTTCTTCAGGGAAGATTTAAA-CGA
65 TGAGGGAAAATCAGATCTAGGGACATTTATTCATTCCACTATTCTTCAGGGAAGA-TCAAATCGA
*
553775 GGCAT
129 GGCAG
* ** *
553780 ACTTGTTCCACTGTTACTTAGGGAATTTCAAATCTTGAAAAGATGGATATGTTCCGTTTTTTCTT
1 ACTTGTTCCACTGTTACTCAGGGAAGATCAAATCTTGAAAAGATGGATATGTTCCGCTTTTTCTT
* * * *
553845 GAGGGAAAATCAGATCTAGGGACGTTTATTTATTCCATTATTCTTCAGGGAATATCAAATCGAGG
66 GAGGGAAAATCAGATCTAGGGACATTTATTCATTCCACTATTCTTCAGGGAAGATCAAATCGAGG
*
553910 TAG
131 CAG
* * * * * *
553913 ACCTGTTCCGCTATT-CTCAAGGAAGATCAAATCTTG-AAAGATAAGATTTTGTTCCGCTTTTTC
1 ACTTGTTCCACTGTTACTCAGGGAAGATCAAATCTTGAAAAGAT-GGA-TATGTTCCGCTTTTTC
* * * * * * * * *
553976 TTTAGGGAATATCAGATCT-GTGAACGTTAATTCATTCTACTATTCCTCATGGAAGATTAAATCG
64 TTGAGGGAAAATCAGATCTAG-GGACATTTATTCATTCCACTATTCTTCAGGGAAGATCAAATCG
554040 AG
128 AG
554042 TTCGATTCAC
Statistics
Matches: 219, Mismatches: 39, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
131 6 0.03
132 24 0.11
133 158 0.72
134 31 0.14
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (133 bp):
ACTTGTTCCACTGTTACTCAGGGAAGATCAAATCTTGAAAAGATGGATATGTTCCGCTTTTTCTT
GAGGGAAAATCAGATCTAGGGACATTTATTCATTCCACTATTCTTCAGGGAAGATCAAATCGAGG
CAG
Found at i:554291 original size:13 final size:14
Alignment explanation
Indices: 554269--554298 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
554259 AATTGGTTAC
554269 TTTTCAAAAAAGAT
1 TTTTCAAAAAAGAT
554283 TTTTC-AAAAAGAT
1 TTTTCAAAAAAGAT
554296 TTT
1 TTT
554299 GATGAGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTTCAAAAAAGAT
Found at i:554376 original size:20 final size:21
Alignment explanation
Indices: 554351--554391 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
554341 ATGCGAAAAC
554351 ATCTTGC-CG-AAGGACTTATA
1 ATCTTGCTCGAAAGG-CTTATA
554371 ATCTTGCTCGAAAGGCTTATA
1 ATCTTGCTCGAAAGGCTTATA
554392 GATGACCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (21 bp):
ATCTTGCTCGAAAGGCTTATA
Found at i:554864 original size:221 final size:221
Alignment explanation
Indices: 554492--555078 Score: 648
Period size: 221 Copynumber: 2.6 Consensus size: 221
554482 AACTTTTCTT
* * * *
554492 ACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAAAAAATTTATC--ATTTTTCAAGAGACATG
1 ACTTTTAAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTT-TCTAATTTTTCGAGAGACATG
** * * *
554555 TGAAAACATCCTGCCCAAAGGTC-TAGTGGA-TG-TCCGAATGACTTATTATCTTGCTCAAATGT
65 TGAAAACAT-CTTACCAAAGGTCTTA-TGGATTGCT-CGAAAGACTTATCATCTTGCTCAAA-GA
* *
554617 CTTACAGATGACTAGAAGGATTTAAGCATGATGCTCGAAAGACTTACAAATGGCCCGAAGGACTT
126 CTTACAGATGACCAGAAGGATTTAAGCATCATGCTCGAAAGACTTACAAATGGCCCGAAGGACTT
*
554682 ACCAATTTTGGAAACAGTTTACTAAGTAAG-
191 ACCAAATTTGGAAACAGTTTACTAAGTAAGA
*
554712 ACTTTTAAAAAAATTCAATTTTTAGATTTAAATGAGAAACTTTTCTAATTTTT-GAGAGACATGT
1 ACTTTTAAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTAATTTTTCGAGAGACATGT
* * *
554776 GAAAACATCTTACTCGAAGGTCTTATGGATTGCTCGGAGGACTTATCATCTTGCTCGAAAGACTT
66 GAAAACATCTTAC-CAAAGGTCTTATGGATTGCTCGAAAGACTTATCATCTTGCTC-AAAGACTT
* * **
554841 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAGAGACTTACTGATGGCCCGAAGGACTTACC
129 ACAGATGACCAGAAGGATTTAAGCATCATGCTCGAAAGACTTACAAATGGCCCGAAGGACTTACC
* * *
554906 AAATTTGGGAATAGTTTACTAGGTAAGAA
194 AAATTTGGAAACAGTTTACTAAGTAAG-A
*
554935 ACTTTTCTTACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTGTTT
1 AC--TT-TTA------AAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCT-A--AT-TTT
* * * * * *
555000 TCGAAATACATGTGAAAACATCATGACCAAAGGTCTTGTGGATTGCCCGAAAAACTTATCATCTT
53 TCGAGAGACATGTGAAAACATC-TTACCAAAGGTCTTATGGATTGCTCGAAAGACTTATCATCTT
555065 GCTCAAAAGACTTA
117 GCTC-AAAGACTTA
555079 TATATGACAC
Statistics
Matches: 309, Mismatches: 34, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
219 5 0.02
220 68 0.22
221 115 0.37
222 4 0.01
223 2 0.01
225 2 0.01
226 3 0.01
232 38 0.12
233 1 0.00
235 1 0.00
236 4 0.01
237 63 0.20
238 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (221 bp):
ACTTTTAAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTAATTTTTCGAGAGACATGT
GAAAACATCTTACCAAAGGTCTTATGGATTGCTCGAAAGACTTATCATCTTGCTCAAAGACTTAC
AGATGACCAGAAGGATTTAAGCATCATGCTCGAAAGACTTACAAATGGCCCGAAGGACTTACCAA
ATTTGGAAACAGTTTACTAAGTAAGA
Found at i:562446 original size:28 final size:31
Alignment explanation
Indices: 562396--562465 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
562386 GAGAACATAG
562396 AAAAAAT-AAATGCTAGAATATTAAA-GGAC
1 AAAAAATAAAATGCTAGAATATTAAAGGGAC
*
562425 -TAAAATAAAATGC-AGGAA-ATTAAAGGGAC
1 AAAAAATAAAATGCTA-GAATATTAAAGGGAC
562454 AAAAAATAAAAT
1 AAAAAATAAAAT
562466 ACTAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
28 12 0.34
29 13 0.37
30 10 0.29
ACGTcount: A:0.61, C:0.06, G:0.14, T:0.19
Consensus pattern (31 bp):
AAAAAATAAAATGCTAGAATATTAAAGGGAC
Found at i:562857 original size:65 final size:66
Alignment explanation
Indices: 562674--562861 Score: 290
Period size: 66 Copynumber: 2.9 Consensus size: 66
562664 TTGAGCAAAT
* * *
562674 AAATAAAATGTTAGTAAGTTAGTATAAACAATAAAATAAAATGTTAGTATGTTAGTACAAACGAT
1 AAATAAAATGTTAGTATGTTAGTACAAACAATAAAATAAAATGTTAGTATGTTAGTACAAACAAT
*
562739 T
66 A
**
562740 AAATAAAATGTTAGTATGTTAGTACAAACAATAAAATAAAATGTTAGTATGTTAGTATGAACAAT
1 AAATAAAATGTTAGTATGTTAGTACAAACAATAAAATAAAATGTTAGTATGTTAGTACAAACAAT
562805 A
66 A
*
562806 AAATAAAATGTT-GTATGTTAATA-AGAACAATAAAATAAAATGTTAGTATGTTAGTA
1 AAATAAAATGTTAGTATGTTAGTACA-AACAATAAAATAAAATGTTAGTATGTTAGTA
562862 GTCAAATTAA
Statistics
Matches: 114, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
64 1 0.01
65 41 0.36
66 72 0.63
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (66 bp):
AAATAAAATGTTAGTATGTTAGTACAAACAATAAAATAAAATGTTAGTATGTTAGTACAAACAAT
A
Found at i:562873 original size:33 final size:32
Alignment explanation
Indices: 562674--562861 Score: 261
Period size: 33 Copynumber: 5.8 Consensus size: 32
562664 TTGAGCAAAT
* *
562674 AAATAAAATGTTAGTAAGTTAGTATAAACAATA
1 AAATAAAATGTTAGTATGTTAGTA-CAACAATA
* *
562707 AAATAAAATGTTAGTATGTTAGTACAAACGATT
1 AAATAAAATGTTAGTATGTTAGTAC-AACAATA
562740 AAATAAAATGTTAGTATGTTAGTACAAACAATA
1 AAATAAAATGTTAGTATGTTAGTAC-AACAATA
*
562773 AAATAAAATGTTAGTATGTTAGTATGAACAATA
1 AAATAAAATGTTAGTATGTTAGTA-CAACAATA
* *
562806 AAATAAAATGTT-GTATGTTAATAAGAACAATA
1 AAATAAAATGTTAGTATGTTAGT-ACAACAATA
562838 AAATAAAATGTTAGTATGTTAGTA
1 AAATAAAATGTTAGTATGTTAGTA
562862 GTCAAATTAA
Statistics
Matches: 142, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
32 30 0.21
33 112 0.79
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (32 bp):
AAATAAAATGTTAGTATGTTAGTACAACAATA
Found at i:564257 original size:3 final size:3
Alignment explanation
Indices: 564249--564317 Score: 59
Period size: 3 Copynumber: 22.7 Consensus size: 3
564239 TGTGAAAATA
* * * * *
564249 AAT AAT AAT AAT ATT AAT -AT AAT GAT ATT AAG AAT ATT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
564294 AAT AAT ATT AAT AAAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AA
564318 AAAATAAAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:564276 original size:14 final size:14
Alignment explanation
Indices: 564253--564313 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 14
564243 AAAATAAATA
564253 ATAATAATATTAAT
1 ATAATAATATTAAT
*
564267 ATAATGATATT-A-
1 ATAATAATATTAAT
* * *
564279 AGAATATTAATAA-
1 ATAATAATATTAAT
564292 ATAATAATATTAAT
1 ATAATAATATTAAT
564306 A-AATAATA
1 ATAATAATA
564314 ATAAAAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
12 7 0.19
13 19 0.51
14 11 0.30
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
ATAATAATATTAAT
Found at i:564302 original size:16 final size:16
Alignment explanation
Indices: 564281--564316 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
564271 TGATATTAAG
564281 AATATTAATAAATAAT
1 AATATTAATAAATAAT
564297 AATATTAATAAATAAT
1 AATATTAATAAATAAT
564313 AATA
1 AATA
564317 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATTAATAAATAAT
Found at i:564486 original size:22 final size:20
Alignment explanation
Indices: 564448--564514 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
564438 TCAACGTATA
564448 AAATTATAAAATAAAATATT
1 AAATTATAAAATAAAATATT
*
564468 AAATTATATTAAATTAAATA-T
1 AAATTATA--AAATAAAATATT
* * *
564489 ATATTA-AAAATATATTATT
1 AAATTATAAAATAAAATATT
*
564508 TAATTAT
1 AAATTAT
564515 GTCAATGTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
18 7 0.19
19 5 0.14
20 9 0.25
21 6 0.17
22 9 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATTATAAAATAAAATATT
Found at i:564493 original size:16 final size:15
Alignment explanation
Indices: 564465--564496 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
564455 AAAATAAAAT
564465 ATTAAATTATATTAA
1 ATTAAATTATATTAA
564480 ATTAAATATATATTAA
1 ATTAAAT-TATATTAA
564496 A
1 A
564497 AATATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAAATTATATTAA
Found at i:569814 original size:20 final size:20
Alignment explanation
Indices: 569786--569825 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
569776 AAACTTATTT
569786 AGTGCTTTGTTATT-GAGATC
1 AGTGCTTTGTT-TTCGAGATC
*
569806 AGTGTTTTGTTTTCGAGATC
1 AGTGCTTTGTTTTCGAGATC
569826 GTTTCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.17, C:0.10, G:0.25, T:0.47
Consensus pattern (20 bp):
AGTGCTTTGTTTTCGAGATC
Found at i:581452 original size:61 final size:65
Alignment explanation
Indices: 581356--581500 Score: 183
Period size: 61 Copynumber: 2.3 Consensus size: 65
581346 CTGCACTAAG
* * * *
581356 CTTACGCTCTAGTACT-ATTCTGTATATTCCACATAAAGTCGTGCCCACCACCTACAC-TAG-GT
1 CTTACACTCTAGTGCTAATTCTGGATATGCCACATAAAGTCGTGCCCACCACCTACACTTAGTGT
* *
581418 -TTACACTCTAGTGCTAATTC-GGATATGCCACATAAGGTTGTGCCCACCACCTACACTTAGTGT
1 CTTACACTCTAGTGCTAATTCTGGATATGCCACATAAAGTCGTGCCCACCACCTACACTTAGTGT
*
581481 CCTTACACACTAGTGCTAAT
1 -CTTACACTCTAGTGCTAAT
581501 ATAAATCTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
61 45 0.63
62 7 0.10
63 2 0.03
65 17 0.24
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.30
Consensus pattern (65 bp):
CTTACACTCTAGTGCTAATTCTGGATATGCCACATAAAGTCGTGCCCACCACCTACACTTAGTGT
Found at i:602705 original size:35 final size:35
Alignment explanation
Indices: 602657--602736 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
602647 CACAATACTC
*
602657 TGTTTCTTGTTATCAAATGCATTTGATAATTGATAG
1 TGTTT-TTTTTATCAAATGCATTTGATAATTGATAG
602693 TGTTTTTTTTATCAAATGCATTTGATAATTGATAG
1 TGTTTTTTTTATCAAATGCATTTGATAATTGATAG
602728 TGTTTTTTT
1 TGTTTTTTT
602737 AGTAGCCATT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 38 0.88
36 5 0.12
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.54
Consensus pattern (35 bp):
TGTTTTTTTTATCAAATGCATTTGATAATTGATAG
Found at i:605525 original size:2 final size:2
Alignment explanation
Indices: 605518--605574 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
605508 CGATAAAAGC
605518 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
605560 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
605575 CTTTCTAACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:607395 original size:46 final size:45
Alignment explanation
Indices: 607345--607442 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
607335 AGCATCCCAA
*
607345 CATGCTTATAATACATCATTATACCATTT-TCATTATGGCA-TCATTT
1 CATGCCTATAATACATCATTATA-CATTTCT-ATTATGGCATTC-TTT
* * * *
607391 CATGCCTCTTATACATTATTATACATTTCTTTTATGGCATTCTTT
1 CATGCCTATAATACATCATTATACATTTCTATTATGGCATTCTTT
607436 CATGCCT
1 CATGCCT
607443 TTTATGTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 23 0.51
46 22 0.49
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (45 bp):
CATGCCTATAATACATCATTATACATTTCTATTATGGCATTCTTT
Found at i:607437 original size:45 final size:46
Alignment explanation
Indices: 607355--607447 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 46
607345 CATGCTTATA
607355 ATACATCATTATACCATTTTCATTATGGCATCATTTCATGCCTCTT
1 ATACATCATTATACCATTTTCATTATGGCATCATTTCATGCCTCTT
* * *
607401 ATACATTATTATA-CA-TTTCTTTTATGGCATTC-TTTCATGCCTTTT
1 ATACATCATTATACCATTTTC-ATTATGGCA-TCATTTCATGCCTCTT
607446 AT
1 AT
607448 GTTTTGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
44 4 0.10
45 24 0.57
46 14 0.33
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.48
Consensus pattern (46 bp):
ATACATCATTATACCATTTTCATTATGGCATCATTTCATGCCTCTT
Found at i:607470 original size:45 final size:46
Alignment explanation
Indices: 607355--607470 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 46
607345 CATGCTTATA
* *
607355 ATACATCATTATACCATTTT-CATTATGGCATCATTTCATGCCTCTT
1 ATACATTATTATA-CATTTTCCTTTATGGCATCATTTCATGCCTCTT
* *
607401 ATACATTATTATACA-TTTCTTTTATGGCATTC-TTTCATGCCTTTT
1 ATACATTATTATACATTTTCCTTTATGGCA-TCATTTCATGCCTCTT
*** *
607446 ATGTTTTGTT-TACATTTTCCTTTAT
1 ATACATTATTATACATTTTCCTTTAT
607471 AACATACATT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
44 7 0.12
45 37 0.64
46 14 0.24
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (46 bp):
ATACATTATTATACATTTTCCTTTATGGCATCATTTCATGCCTCTT
Found at i:607523 original size:4 final size:4
Alignment explanation
Indices: 607514--608603 Score: 2069
Period size: 4 Copynumber: 275.2 Consensus size: 4
607504 CATTATATAA
607514 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
607562 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
607610 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
607658 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
607704 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
607752 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
607800 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
607848 ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
607894 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-AT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
607941 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACTAC ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT
607990 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608038 ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608084 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608132 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608180 AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
608226 ACAT ACCT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608274 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608321 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608369 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608417 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608465 AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608511 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608559 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
608604 TACATATTTG
Statistics
Matches: 1069, Mismatches: 4, Indels: 26
0.97 0.00 0.02
Matches are distributed among these distances:
2 10 0.01
3 6 0.01
4 1050 0.98
5 3 0.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:609312 original size:59 final size:60
Alignment explanation
Indices: 609123--609328 Score: 360
Period size: 60 Copynumber: 3.5 Consensus size: 60
609113 TCCTATACGA
* * * *
609123 AAATTCATACACTTAGTATGATCTCCTTATCATTTTAGCATAGAAAGTTCCCTTATCTAG
1 AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAGAAAGTGCCCTTATCTGG
609183 AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAGAAAGTGCCCTTATCTGG
1 AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAGAAAGTGCCCTTATCTGG
*
609243 AAATTCATACACTTAGTATGATTTCCTTATCATTTT-GCACACAAAGTGCCCTTATCTGG
1 AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAGAAAGTGCCCTTATCTGG
609302 AAATTCATACACTTAGTATGATTTCCT
1 AAATTCATACACTTAGTATGATTTCCT
609329 CTTTTATGTT
Statistics
Matches: 141, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 49 0.35
60 92 0.65
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (60 bp):
AAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAGAAAGTGCCCTTATCTGG
Found at i:609480 original size:79 final size:79
Alignment explanation
Indices: 609368--609650 Score: 408
Period size: 79 Copynumber: 3.6 Consensus size: 79
609358 TTTCAACTTT
* * * * *
609368 GGCATCCTTTCATGCCAATAATGTACCCATATGCATTATTCTGTTATACCGATAATGTACCCATA
1 GGCATCCTTTCATGCCATTAATGCACCTATATGCATTATTCTTTTATGCCGATAATGTACCCATA
609433 TACATATCAGCTAA
66 TACATATCAGCTAA
* * ** *
609447 GGCATCCTTTCATGCCATTAATACACCTGTATGCATTATTCTTTTATGTTGATAATGTACTCATA
1 GGCATCCTTTCATGCCATTAATGCACCTATATGCATTATTCTTTTATGCCGATAATGTACCCATA
*
609512 TACATATCAGTTAA
66 TACATATCAGCTAA
* *
609526 GGCATCCTTTCAAGCCATTAATTCA-CTCATATGCATTATTCTTTTATGCCGATAATGTACCCAT
1 GGCATCCTTTCATGCCATTAATGCACCT-ATATGCATTATTCTTTTATGCCGATAATGTACCCAT
*
609590 ACACATATCAGCTAA
65 ATACATATCAGCTAA
*
609605 GGCATCCTTTCATGCCATTAATGCACC-ATGTGCATTATTCTTTTAT
1 GGCATCCTTTCATGCCATTAATGCACCTATATGCATTATTCTTTTAT
609651 TCATTAGTTT
Statistics
Matches: 180, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
78 20 0.11
79 159 0.88
80 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (79 bp):
GGCATCCTTTCATGCCATTAATGCACCTATATGCATTATTCTTTTATGCCGATAATGTACCCATA
TACATATCAGCTAA
Found at i:609605 original size:158 final size:157
Alignment explanation
Indices: 609328--609650 Score: 463
Period size: 158 Copynumber: 2.1 Consensus size: 157
609318 TATGATTTCC
** * * *
609328 TCTTTTATGTTGATAATGCACCCATATGTATTTCAACTTTGGCATCCTTTCATGCCAATAATGTA
1 TCTTTTATGTTGATAATGCACCCATATACATATCAACTTAGGCATCCTTTCAAGCCAATAATGTA
*
609393 CCCATATGCATTATTCTGTTATACCGATAATGTACCCATATACATATCAGCTAAGGCATCCTTTC
66 CCCATATGCATTATTCTGTTATACCGATAATGTACCCATACACATATCAGCTAAGGCATCCTTTC
609458 ATGCCATTAATACACC-TGTATGCATTAT
131 ATGCCATTAATACACCATG--TGCATTAT
* * * *
609486 TCTTTTATGTTGATAATGTACTCATATACATATC-AGTTAAGGCATCCTTTCAAGCCATTAAT-T
1 TCTTTTATGTTGATAATGCACCCATATACATATCAACTT-AGGCATCCTTTCAAGCCAATAATGT
* * *
609549 CACTCATATGCATTATTCTTTTATGCCGATAATGTACCCATACACATATCAGCTAAGGCATCCTT
65 -ACCCATATGCATTATTCTGTTATACCGATAATGTACCCATACACATATCAGCTAAGGCATCCTT
*
609614 TCATGCCATTAATGCACCATGTGCATTAT
129 TCATGCCATTAATACACCATGTGCATTAT
609643 TCTTTTAT
1 TCTTTTAT
609651 TCATTAGTTT
Statistics
Matches: 148, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
157 20 0.14
158 126 0.85
159 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.38
Consensus pattern (157 bp):
TCTTTTATGTTGATAATGCACCCATATACATATCAACTTAGGCATCCTTTCAAGCCAATAATGTA
CCCATATGCATTATTCTGTTATACCGATAATGTACCCATACACATATCAGCTAAGGCATCCTTTC
ATGCCATTAATACACCATGTGCATTAT
Found at i:610087 original size:22 final size:21
Alignment explanation
Indices: 610034--610089 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
610024 TTGGCCCTTT
* *
610034 GGTATCAATACCCCTGCTTAT
1 GGTATCAATACCCCTGATTAG
* * *
610055 GGCATTAATACCACCTTATTAG
1 GGTATCAATACC-CCTGATTAG
610077 GGTATCAATACCC
1 GGTATCAATACCC
610090 TCTTCATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (21 bp):
GGTATCAATACCCCTGATTAG
Found at i:610175 original size:22 final size:20
Alignment explanation
Indices: 610128--610203 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
610118 TCGATGTAAC
* *
610128 ATGGTATCAATACCCTCA-CC
1 ATGGTATCGATACCC-CATCT
*
610148 ATGGTATCGATACCCCTATGTT
1 ATGGTATCGATACCCC-AT-CT
610170 ATGGTATCGATACCCCATCT
1 ATGGTATCGATACCCCATCT
610190 A-GGTATCGATACCC
1 ATGGTATCGATACCC
610204 AAATTAGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
19 14 0.29
20 17 0.35
21 2 0.04
22 16 0.33
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGGTATCGATACCCCATCT
Found at i:610196 original size:19 final size:22
Alignment explanation
Indices: 610148--610203 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
610138 TACCCTCACC
*
610148 ATGGTATCGATACCCCTATGTT
1 ATGGTATCGATACCCCTATGCT
610170 ATGGTATCGATACCCC-AT-CT
1 ATGGTATCGATACCCCTATGCT
610190 A-GGTATCGATACCC
1 ATGGTATCGATACCC
610204 AAATTAGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 13 0.39
20 2 0.06
21 2 0.06
22 16 0.48
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (22 bp):
ATGGTATCGATACCCCTATGCT
Found at i:612014 original size:18 final size:17
Alignment explanation
Indices: 611991--612025 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
611981 TAAAAACAGT
611991 AAATAAAAAGATAAATAA
1 AAATAAAAAGA-AAATAA
*
612009 AAATAAGAAGAAAATAA
1 AAATAAAAAGAAAATAA
612026 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (17 bp):
AAATAAAAAGAAAATAA
Found at i:618984 original size:17 final size:16
Alignment explanation
Indices: 618962--618995 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
618952 TAAAAACAGT
618962 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
618979 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
618995 A
1 A
618996 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:621931 original size:17 final size:17
Alignment explanation
Indices: 621909--621948 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
621899 TCTATGAGTT
*
621909 TTAATTTAACCCTTAGA
1 TTAATTTAACCCTAAGA
*
621926 TTAATTTAACCCTAATA
1 TTAATTTAACCCTAAGA
621943 TTAATT
1 TTAATT
621949 AGTATATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAATTTAACCCTAAGA
Found at i:623544 original size:3 final size:3
Alignment explanation
Indices: 623536--623577 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
623526 TTCGGGTCGA
623536 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
623578 TATTATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:623582 original size:3 final size:3
Alignment explanation
Indices: 623576--623619 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
623566 AATAATAATA
623576 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
623620 AACAATTACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:624592 original size:10 final size:9
Alignment explanation
Indices: 624561--624590 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
624551 AAATCTAATT
624561 AAAAT-GAA
1 AAAATGGAA
624569 AAAATGGAA
1 AAAATGGAA
624578 AAAATGGAA
1 AAAATGGAA
624587 AAAA
1 AAAA
624591 ATAAAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (9 bp):
AAAATGGAA
Found at i:627857 original size:20 final size:20
Alignment explanation
Indices: 627832--627876 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
627822 TCAGGGGCAT
627832 GGACAATCGAAGAATGATAG
1 GGACAATCGAAGAATGATAG
627852 GGACAATCGAAGAATGATAG
1 GGACAATCGAAGAATGATAG
627872 GGACA
1 GGACA
627877 TTGCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.31, T:0.13
Consensus pattern (20 bp):
GGACAATCGAAGAATGATAG
Found at i:628540 original size:13 final size:13
Alignment explanation
Indices: 628522--628546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
628512 TTCATGTGAA
628522 TAAAAATTTATCC
1 TAAAAATTTATCC
628535 TAAAAATTTATC
1 TAAAAATTTATC
628547 ACCCTGGGGA
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAAATTTATCC
Found at i:628850 original size:18 final size:18
Alignment explanation
Indices: 628822--628856 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
628812 AACAAAGAGA
628822 AAAGTAGCAAAGGAAAAAC
1 AAAGTAGCAAA-GAAAAAC
628841 AAAG-AGCAAAGAAAAA
1 AAAGTAGCAAAGAAAAA
628857 AATCAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.69, C:0.09, G:0.20, T:0.03
Consensus pattern (18 bp):
AAAGTAGCAAAGAAAAAC
Found at i:628857 original size:18 final size:19
Alignment explanation
Indices: 628822--628857 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
628812 AACAAAGAGA
*
628822 AAAGTAGCAAAGGAAAAAC
1 AAAGTAGCAAAGAAAAAAC
628841 AAAG-AGCAAAGAAAAAA
1 AAAGTAGCAAAGAAAAAA
628858 ATCAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.69, C:0.08, G:0.19, T:0.03
Consensus pattern (19 bp):
AAAGTAGCAAAGAAAAAAC
Found at i:628871 original size:20 final size:19
Alignment explanation
Indices: 628835--628873 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
628825 GTAGCAAAGG
**
628835 AAAAACAAAGAGCAAAGAA
1 AAAAACAAAGAAAAAAGAA
628854 AAAAATCAAAGAAAAAAGAA
1 AAAAA-CAAAGAAAAAAGAA
628874 GACAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.03
Consensus pattern (19 bp):
AAAAACAAAGAAAAAAGAA
Found at i:630255 original size:65 final size:65
Alignment explanation
Indices: 630074--630262 Score: 260
Period size: 65 Copynumber: 3.0 Consensus size: 65
630064 ATCAGTATCC
* * * * *
630074 TTTGAGT-TGTTTATTTTGAAAC-AAATTTTGTCTCTC--GAGACAGTTTCTTTTAAAAAAAATC
1 TTTGAGTATGTTTATTTAGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAATA
* * *
630135 TTTGAGTATGTTTATCTAGAAACAAAGTTTTATCTCTCTTGAGACAATTTCTTTTGAGAAAAATA
1 TTTGAGTATGTTTATTTAGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAATA
*
630200 TTTGAGTATGTTTATTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGGAGAAAA
1 TTTGAGTATGTTTATTTAGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTT-GAGAAAA
630263 GACCATCTTT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
61 7 0.06
62 13 0.12
63 12 0.11
65 72 0.65
66 7 0.06
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (65 bp):
TTTGAGTATGTTTATTTAGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAATA
Found at i:630786 original size:135 final size:131
Alignment explanation
Indices: 630389--630794 Score: 372
Period size: 131 Copynumber: 3.1 Consensus size: 131
630379 TGAAACTATT
* * * * * * * **
630389 ACCCCTAGATAATCAGCTGTCCTCATCACGTATGAACCG-TGTTATCATCCCTAGAGATGGC-CT
1 ACCCTTAGATAACCAGCAGTCCTCATCACGAAGGAA-CGATGTTATCACCCCTAAAGATGGCAAG
** * * * *
630452 ACAGTCCTCATCATGTAGGAACCGTGTCATACCCCGACCATACCTCCTCATCACGTAGGAGTCGT
65 ACA-TCCTCATCACATAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGT
630517 GTC
129 GTC
* * * ** * * *
630520 ACCCTTAGATAACCAGGAGTCCTTATCACGTAGGAATTATGTTATCATCCCTAAAGATGGCATGC
1 ACCCTTAGATAACCAGCAGTCCTCATCACGAAGGAACGATGTTATCACCCCTAAAGATGGCAAGA
* * * *
630585 CATCCTCATCGCATAGGAACCGTGTCATCCTCCGATCAGACCTCCTCATCACGTAGGAGCCGTGT
66 CATCCTCATCACATAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGT
630650 C
131 C
* *
630651 ATCCC-TAGATAACCAGCCGTCCTCATCGCGAAGGAACCGA-GTTATCACCCTCTTTAAAGATGG
1 A-CCCTTAGATAACCAGCAGTCCTCATCACGAAGGAA-CGATGTTATCACCC-C--TAAAGATGG
* * * *
630714 CTAAGA-ACTCTTCATCACATATGAGCAGTGTCATCCCCCGACCAGATCTCCTCATCACGTAGGA
61 C-AAGACA-TCCTCATCACATAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGA
* *
630778 GGCATGTC
124 GCCGTGTC
*
630786 ACTCTTAGA
1 ACCCTTAGA
630795 CGACCAGAAC
Statistics
Matches: 224, Mismatches: 41, Indels: 16
0.80 0.15 0.06
Matches are distributed among these distances:
131 143 0.64
132 7 0.03
134 13 0.06
135 61 0.27
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (131 bp):
ACCCTTAGATAACCAGCAGTCCTCATCACGAAGGAACGATGTTATCACCCCTAAAGATGGCAAGA
CATCCTCATCACATAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGT
C
Found at i:630992 original size:3 final size:3
Alignment explanation
Indices: 630984--631009 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
630974 GTAGAAAAAA
630984 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
631010 ATAATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:631017 original size:9 final size:9
Alignment explanation
Indices: 630982--631022 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
630972 AAGTAGAAAA
630982 AATATTATT
1 AATATTATT
*
630991 ATTATTATT
1 AATATTATT
*
631000 ATTATTATT
1 AATATTATT
*
631009 AATAATATT
1 AATATTATT
631018 AATAT
1 AATAT
631023 AACAATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATATTATT
Found at i:632902 original size:15 final size:15
Alignment explanation
Indices: 632882--632910 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
632872 CGCTTTTCAC
632882 TTTTATTTTGTTTTG
1 TTTTATTTTGTTTTG
632897 TTTTATTTTGTTTT
1 TTTTATTTTGTTTT
632911 ATCTTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (15 bp):
TTTTATTTTGTTTTG
Found at i:634348 original size:7 final size:7
Alignment explanation
Indices: 634336--634362 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
634326 TATTAATCAA
634336 AAATATT
1 AAATATT
634343 AAATATT
1 AAATATT
634350 AAATATT
1 AAATATT
634357 AAATAT
1 AAATAT
634363 GTTATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATATT
Found at i:638839 original size:2 final size:2
Alignment explanation
Indices: 638834--638876 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
638824 AAAAAAACTG
638834 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
638876 A
1 A
638877 GGCTTTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:642515 original size:54 final size:54
Alignment explanation
Indices: 642401--642986 Score: 602
Period size: 54 Copynumber: 10.9 Consensus size: 54
642391 CTGAATAACA
* ** * ** *
642401 TGCTCTACTCCTCCATAACAAAGGAA-GATAGAGCTCGCTTGGTCTTAAAAATA
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTTGGAAATT
* ** *
642454 TGTTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTAC-CTGGTCTTAAAAAAT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTC-GGTCTTGGAAATT
* * * * * * *
642508 GGCTCTACTTCTTCATAACAAAGGAACACTA-AGGCTTAATCAGTCTTGGAAGTT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGA-GCTTACTCGGTCTTGGAAATT
* * * *
642562 TGCCCTGCTCCTCTATAACAAAGGAACGCTAGAGCTTACTCGATCTTGGAAATT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTTGGAAATT
* * * ** *
642616 TGATCTACTCCTCCATAACAAAGGAACTCTAGAGCTTACTCAGTCTTAAAAAAT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTTGGAAATT
* * ** * * * *
642670 GGCTTTACTCCTCTTTAACTAAGGAACGATAGAGTTTACTCGATCTTGGAAATT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTTGGAAATT
* * *
642724 TGATCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGATCTTGAAAATT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTTGGAAATT
** * * * * *
642778 TATTGTACTCCTCTATAACAAGGGAACGGTAGAGCTTACTTGGTCTTGGAAATT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTTGGAAATT
* * * * *
642832 TTCTATACTCCTCCATAACAAAGGAACACTAGAGCTTAGTCGGTCTTAGAAATT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTTGGAAATT
** ** * *
642886 TTTTCTACTTTTCCATAACAAAGGAACGCTAGAGCTTATTCGATCTTGGAAATT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTTGGAAATT
* *
642940 TGCTCTACTCCTCCATAACAAAGAAACACTAGAGCTTACTCGGTCTT
1 TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTT
642987 TAAAAAATGT
Statistics
Matches: 431, Mismatches: 97, Indels: 9
0.80 0.18 0.02
Matches are distributed among these distances:
53 26 0.06
54 403 0.94
55 2 0.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (54 bp):
TGCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCGGTCTTGGAAATT
Found at i:646028 original size:17 final size:17
Alignment explanation
Indices: 646006--646051 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
645996 AAAGTCAAAA
646006 TTCAGTGGCTCGTAATC
1 TTCAGTGGCTCGTAATC
*
646023 TTCAGTGGCTCATAATC
1 TTCAGTGGCTCGTAATC
*
646040 TTCTGTGGCTCG
1 TTCAGTGGCTCG
646052 ATTTGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (17 bp):
TTCAGTGGCTCGTAATC
Found at i:650742 original size:42 final size:41
Alignment explanation
Indices: 650653--650750 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 41
650643 GTCTTAGAAT
* **
650653 GGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAAAG
1 GGCCCGAAGGACTTATCATCATGCTCGAAAAACTTATAAAG
* * *
650694 GACCCGAAGGATTTATGCATCATGCTCGAAAAACTTACT-GAG
1 GGCCCGAAGGACTTAT-CATCATGCTCGAAAAACTTA-TAAAG
650736 GGCCCGAAGGACTTA
1 GGCCCGAAGGACTTA
650751 CTAAGTAGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 14 0.30
42 32 0.68
43 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (41 bp):
GGCCCGAAGGACTTATCATCATGCTCGAAAAACTTATAAAG
Found at i:650959 original size:42 final size:41
Alignment explanation
Indices: 650884--650965 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
650874 CCCAAATGTC
* * *
650884 TTATGGATGACCCGAATGACTTATCATCTTGCTCGAAAGAG
1 TTATAGATGACCCGAAGGACTTATCATCATGCTCGAAAGAG
**
650925 TTATAGATGACCCGAAGGGTTTAATCATCATGCTCGAAAGA
1 TTATAGATGACCCGAAGGACTT-ATCATCATGCTCGAAAGA
650966 CTTACGAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 18 0.51
42 17 0.49
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (41 bp):
TTATAGATGACCCGAAGGACTTATCATCATGCTCGAAAGAG
Found at i:650960 original size:239 final size:239
Alignment explanation
Indices: 650382--650991 Score: 749
Period size: 240 Copynumber: 2.5 Consensus size: 239
650372 GAACACCATA
* * * * * *
650382 TGAAAACATCCTGCCCGAAGGTCTTACATATGGCTCGAAGGACTTATCATCTTGCTTGAAAGGCT
1 TGAAAACATCCAGCCCAAAGGTCTTAGA-ATGACCCGAAGGACTTATCATCTTGCTCGAAAGGCT
** *
650447 TATAGATGACCCGAAGGATTTAGGCATCATGCTC-AAAAGACTTACTGATGGCCCGAATGG-CTT
65 TATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAA-ACTTACTGAAGGCCCGAA-GGACTT
* *
650510 ACTGAGTTAGAAAATTTGGAAGTCATTTTCTTACTTTTCAAAAACAATACATTTTCAAAAAAGAT
128 ACTAAGTTAGAAAATTTGGAAATCATTTTCTTACTTTTCAAAAACAATACATTTTCAAAAAAGAT
*
650575 TTAAATAAGAAACTTTGGAAATGGCTTTCTCATTTTTCAAAAATCATT
193 TTAAATAAGAAACTTTGGAAAT-GCTTTCTCATTTTTCAAAAATCATG
* *
650623 TGAAAACATCCAGCCCGAAGGTCTTAGAATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTT
1 TGAAAACATCCAGCCCAAAGGTCTTAGAATGACCCGAAGGACTTATCATCTTGCTCGAAAGGCTT
* * *
650688 ATAAAGGACCCGAAGGATTT-ATGCATCATGCTCGAAAAACTTACTGAGGGCCCGAAGGACTTAC
66 ATAGATGACCCGAAGGATTTAAT-CATCATGCTCGAAAAACTTACTGAAGGCCCGAAGGACTTAC
** **
650752 TAAG-TAGGAATCTTTGGAAATCATTTTCTTACTTTTC-AAAA-AAT-CAATTTTCAGGAAAGAT
130 TAAGTTA-GAAAATTTGGAAATCATTTTCTTACTTTTCAAAAACAATAC-ATTTTCAAAAAAGAT
* *
650813 TTAAATGAGAAACTTTGGAAAT-CATTTTTCATTTTTTTC-AAAATCATG
193 TTAAATAAGAAACTTTGGAAATGC-TTTCTCA--TTTTTCAAAAATCATG
* * *
650861 TGAAAACA-CCATGCCCAAATGTCTTATGGATGACCCGAATGACTTATCATCTTGCTCGAAAGAG
1 TGAAAACATCCA-GCCCAAAGGTCTTA-GAATGACCCGAAGGACTTATCATCTTGCTCGAAAG-G
* * *
650925 -TTATAGATGACCCGAAGGGTTTAATCATCATGCTCGAAAGACTTAC-GAAAGGCCCAAAGGACT
63 CTTATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAAACTTACTG-AAGGCCCGAAGGACT
650988 TACT
127 TACT
650992 CATCAAGAAA
Statistics
Matches: 327, Mismatches: 29, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
236 1 0.00
237 10 0.03
238 66 0.20
239 102 0.31
240 118 0.36
241 30 0.09
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (239 bp):
TGAAAACATCCAGCCCAAAGGTCTTAGAATGACCCGAAGGACTTATCATCTTGCTCGAAAGGCTT
ATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAAACTTACTGAAGGCCCGAAGGACTTACT
AAGTTAGAAAATTTGGAAATCATTTTCTTACTTTTCAAAAACAATACATTTTCAAAAAAGATTTA
AATAAGAAACTTTGGAAATGCTTTCTCATTTTTCAAAAATCATG
Found at i:651214 original size:58 final size:58
Alignment explanation
Indices: 651151--651334 Score: 226
Period size: 58 Copynumber: 3.2 Consensus size: 58
651141 TGGACTTAAC
* * *
651151 TTCTTTAAATTTCATTTGAAAACATCATGTCAAGAAACCTCTGAAGATCAGACCTAGT
1 TTCTTTAAAATTCATTTGAAAACATCATGTCAAGAAACCTCTGAAAATCAGACTTAGT
* * * *
651209 TTCTTTAAAAATTCTTTTGAAAACATCATGCCAAAAAACCTTTGAAAATCAGACTTAGT
1 TTCTTT-AAAATTCATTTGAAAACATCATGTCAAGAAACCTCTGAAAATCAGACTTAGT
* * * * * *
651268 TTTTTTAAAATGCATTTGAAAATA-CAATGTCAAGAAACCTCTAAAAATCATACTTATT
1 TTCTTTAAAATTCATTTGAAAACATC-ATGTCAAGAAACCTCTGAAAATCAGACTTAGT
651326 TTCTTTAAA
1 TTCTTTAAA
651335 GATATCATAT
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
57 1 0.01
58 55 0.52
59 50 0.47
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (58 bp):
TTCTTTAAAATTCATTTGAAAACATCATGTCAAGAAACCTCTGAAAATCAGACTTAGT
Found at i:651232 original size:59 final size:59
Alignment explanation
Indices: 651065--651334 Score: 223
Period size: 58 Copynumber: 4.6 Consensus size: 59
651055 TGAGTAATCA
* * * * * *
651065 TCAAGAAACCTCTAAAAATCATACTTA-TCTTTTTTAAAAACTCATGTGGAGAA-ATCA--
1 TCAAGAAACCTCTGAAAATCAGACTTAGT-TTCTTTAAAAATTCAT-TTGAAAACATCATG
* * ** ** *
651122 TCACA-AAACATCTAAAAATTGGACTTAACTTCTTT-AAATTTCATTTGAAAACATCATG
1 TCA-AGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAAATTCATTTGAAAACATCATG
* * *
651180 TCAAGAAACCTCTGAAGATCAGACCTAGTTTCTTTAAAAATTCTTTTGAAAACATCATG
1 TCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAAATTCATTTGAAAACATCATG
* * * * * *
651239 CCAAAAAACCTTTGAAAATCAGACTTAGTTT-TTTTAAAATGCATTTGAAAATA-CAATG
1 TCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAAATTCATTTGAAAACATC-ATG
* * *
651297 TCAAGAAACCTCTAAAAATCATACTTATTTTCTTTAAA
1 TCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAA
651335 GATATCATAT
Statistics
Matches: 168, Mismatches: 36, Indels: 16
0.76 0.16 0.07
Matches are distributed among these distances:
55 5 0.03
56 11 0.07
57 28 0.17
58 72 0.43
59 52 0.31
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (59 bp):
TCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAAATTCATTTGAAAACATCATG
Found at i:660636 original size:18 final size:19
Alignment explanation
Indices: 660606--660641 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
660596 TTTTTTTTTG
660606 TAATTTAAAATAATAATAA
1 TAATTTAAAATAATAATAA
660625 TAATTT-AAATAATAATA
1 TAATTTAAAATAATAATA
660642 TAGAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATTTAAAATAATAATAA
Found at i:660637 original size:12 final size:13
Alignment explanation
Indices: 660620--660654 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
660610 TTAAAATAAT
*
660620 AATAATAATTTA-
1 AATAATAATATAG
660632 AATAATAATATAG
1 AATAATAATATAG
660645 AATAATAATA
1 AATAATAATA
660655 GTAAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (13 bp):
AATAATAATATAG
Found at i:660654 original size:13 final size:12
Alignment explanation
Indices: 660620--660659 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
660610 TTAAAATAAT
*
660620 AATAATAATTTA
1 AATAATAATATA
660632 AATAATAATATA
1 AATAATAATATA
660644 GAATAATAATAGTA
1 -AATAATAATA-TA
660658 AA
1 AA
660660 ATGAAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 11 0.44
13 12 0.48
14 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (12 bp):
AATAATAATATA
Found at i:661486 original size:41 final size:41
Alignment explanation
Indices: 661429--661535 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 41
661419 GGATTTCTCA
661429 AAGGACTTATCATCTTGCTCGAAAGAATTATAAATGACCCG
1 AAGGACTTATCATCTTGCTCGAAAGAATTATAAATGACCCG
* * *
661470 AAGGACTTGTCATCTTGCTCGAAAGAGTTATAAATGACTCG
1 AAGGACTTATCATCTTGCTCGAAAGAATTATAAATGACCCG
* * *
661511 AAGGATTTAAGCATCATGCTCGAAA
1 AAGGACTT-ATCATCTTGCTCGAAA
661536 AACTTACTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
41 45 0.78
42 13 0.22
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (41 bp):
AAGGACTTATCATCTTGCTCGAAAGAATTATAAATGACCCG
Found at i:661764 original size:58 final size:59
Alignment explanation
Indices: 661690--661844 Score: 181
Period size: 59 Copynumber: 2.6 Consensus size: 59
661680 ATATGAATCA
* * *
661690 TCAAGAAA-CTTCTGAAAAT-AGGACTTAACTTCTTT-AAATTTCATTTGAAAAAATCATG
1 TCAAGAAACCTT-TGAAAATCA-GACTTAACTTCTTTAAAAATGCATTTGAAAAAACCATG
* ** *
661748 TCAAGAAACCTTTGAAAATCATACTTAGTTTCTTTAAAAATGCATTTGAAAACACCATG
1 TCAAGAAACCTTTGAAAATCAGACTTAACTTCTTTAAAAATGCATTTGAAAAAACCATG
* * *
661807 TCAAGAAACCTTTGAAAATCAAACTTAATTTATTTAAA
1 TCAAGAAACCTTTGAAAATCAGACTTAACTTCTTTAAA
661845 GATATCACAT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 26 0.31
59 58 0.69
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (59 bp):
TCAAGAAACCTTTGAAAATCAGACTTAACTTCTTTAAAAATGCATTTGAAAAAACCATG
Found at i:661814 original size:59 final size:59
Alignment explanation
Indices: 661731--661844 Score: 183
Period size: 59 Copynumber: 1.9 Consensus size: 59
661721 CTTTAAATTT
* * * *
661731 CATTTGAAAAAATCATGTCAAGAAACCTTTGAAAATCATACTTAGTTTCTTTAAAAATG
1 CATTTGAAAAAACCATGTCAAGAAACCTTTGAAAATCAAACTTAATTTATTTAAAAATG
*
661790 CATTTGAAAACACCATGTCAAGAAACCTTTGAAAATCAAACTTAATTTATTTAAA
1 CATTTGAAAAAACCATGTCAAGAAACCTTTGAAAATCAAACTTAATTTATTTAAA
661845 GATATCACAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (59 bp):
CATTTGAAAAAACCATGTCAAGAAACCTTTGAAAATCAAACTTAATTTATTTAAAAATG
Found at i:663414 original size:2 final size:2
Alignment explanation
Indices: 663407--663449 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
663397 AACTTTATTG
663407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
663448 TA
1 TA
663450 ATTTTCTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:666360 original size:13 final size:13
Alignment explanation
Indices: 666342--666366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
666332 AAACCTTTCT
666342 TCGTGAATCGTTG
1 TCGTGAATCGTTG
666355 TCGTGAATCGTT
1 TCGTGAATCGTT
666367 AATCGTTAAT
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:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (13 bp):
TCGTGAATCGTTG
Found at i:671866 original size:2 final size:2
Alignment explanation
Indices: 671859--671930 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
671849 TGACAAAATA
671859 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
671901 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
671931 GCGAATGTAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:673133 original size:20 final size:21
Alignment explanation
Indices: 673108--673161 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
673098 GATAGGTTTT
673108 GGATTGATCCCTTCA-CAAAA
1 GGATTGATCCCTTCACCAAAA
*
673128 GGATTGACCCCTTCACCAAAA
1 GGATTGATCCCTTCACCAAAA
*
673149 GGATAGATCCCTT
1 GGATTGATCCCTT
673162 TCTTACAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (21 bp):
GGATTGATCCCTTCACCAAAA
Found at i:676282 original size:4 final size:4
Alignment explanation
Indices: 676275--676302 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
676265 ATAAATAAAT
676275 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
676303 GAAAAGTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:676900 original size:20 final size:21
Alignment explanation
Indices: 676875--676925 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
676865 ATTGAAATAA
* *
676875 TATCGATACTGATGTGG-AGG
1 TATCGATACTGAAGAGGAAGG
*
676895 TATCGATAC-CAAGAGGAAGG
1 TATCGATACTGAAGAGGAAGG
676915 TATCGATACTG
1 TATCGATACTG
676926 TAATTGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (21 bp):
TATCGATACTGAAGAGGAAGG
Found at i:677823 original size:23 final size:23
Alignment explanation
Indices: 677785--677909 Score: 99
Period size: 23 Copynumber: 5.3 Consensus size: 23
677775 AATCGAGGGT
* *
677785 TCTACGTGATCTTTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* * *
677808 TCTATGTGGTCCTTCGAGACAAT
1 TCTACGTGGTCCTTCGGGACAAA
* *
677831 TCTACATGGTCCTTCAGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* * *
677854 TTCTAGGTGGTCTTTCGGGAAAAA
1 -TCTACGTGGTCCTTCGGGACAAA
* **
677878 TCTACATGGAACTTCGGTG-CAAA
1 TCTACGTGGTCCTTCGG-GACAAA
677901 TTCTACGTG
1 -TCTACGTG
677910 ACACTTCAAT
Statistics
Matches: 77, Mismatches: 22, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
23 51 0.66
24 26 0.34
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAA
Found at i:682508 original size:22 final size:23
Alignment explanation
Indices: 682468--682510 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
682458 AGTTTCCTGA
*
682468 GAGTTGGTTTTTCCTTTCATTTT
1 GAGTTGGTTTTTCCGTTCATTTT
*
682491 GAGTTGGTTTTT-GGTTCATT
1 GAGTTGGTTTTTCCGTTCATT
682511 GTTGGTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.09, C:0.09, G:0.23, T:0.58
Consensus pattern (23 bp):
GAGTTGGTTTTTCCGTTCATTTT
Found at i:682991 original size:21 final size:21
Alignment explanation
Indices: 682967--683021 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
682957 TAATGAACAT
* *
682967 TATCGATATTGATTGAAGTAG
1 TATCGATACTGATTGAAGTAA
682988 TATCGATACTGATTGAAGTAA
1 TATCGATACTGATTGAAGTAA
*
683009 TATTGATACTGAT
1 TATCGATACTGAT
683022 GTGGAGGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (21 bp):
TATCGATACTGATTGAAGTAA
Found at i:683947 original size:23 final size:23
Alignment explanation
Indices: 683916--684046 Score: 136
Period size: 23 Copynumber: 5.7 Consensus size: 23
683906 AGTCGAGGGT
** *
683916 TCTACGTGGTATTTCAGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* * *
683939 TCTATGTGGTCCATCGGGACAAT
1 TCTACGTGGTCCTTCGGGACAAA
** *
683962 TCTATATGGTCCTTCGGGACAAT
1 TCTACGTGGTCCTTCGGGACAAA
* *
683985 TCTATGTGGTCTTTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
*
684008 TACTACGTGGTCCTTTGGGACAAA
1 T-CTACGTGGTCCTTCGGGACAAA
*
684032 TCTACGTGGTACTTC
1 TCTACGTGGTCCTTC
684047 AGTGTAAATT
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
23 71 0.78
24 20 0.22
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAA
Found at i:683989 original size:46 final size:47
Alignment explanation
Indices: 683932--684041 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 47
683922 TGGTATTTCA
* *
683932 GGACAAATCTATGTGGTCCATCGGGAC-AATTCTATATGGTCCTTCG
1 GGACAAATCTATGTGGTCCATCGGGACAAATACTACATGGTCCTTCG
* ** * *
683978 GGACAATTCTATGTGGTCTTTCGGGACAAATACTACGTGGTCCTTTG
1 GGACAAATCTATGTGGTCCATCGGGACAAATACTACATGGTCCTTCG
*
684025 GGACAAATCTACGTGGT
1 GGACAAATCTATGTGGT
684042 ACTTCAGTGT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 24 0.44
47 30 0.56
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (47 bp):
GGACAAATCTATGTGGTCCATCGGGACAAATACTACATGGTCCTTCG
Found at i:684064 original size:24 final size:24
Alignment explanation
Indices: 684028--684080 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
684018 TCCTTTGGGA
*
684028 CAAA-TCTACGTGGTACTTCAGTG
1 CAAATTCTACGTGGCACTTCAGTG
* *
684051 TAAATTCTACGTGGCACTTTAGTG
1 CAAATTCTACGTGGCACTTCAGTG
684075 CAAATT
1 CAAATT
684081 ATATGAGCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (24 bp):
CAAATTCTACGTGGCACTTCAGTG
Found at i:690062 original size:23 final size:23
Alignment explanation
Indices: 690036--690130 Score: 113
Period size: 23 Copynumber: 4.1 Consensus size: 23
690026 GGTTCTACGC
*
690036 GGTCCTTTGGGACAATTCTATGT
1 GGTCCTTTGGGAAAATTCTATGT
*
690059 GGTCCTTTGGGAAAATTCTACGT
1 GGTCCTTTGGGAAAATTCTATGT
*
690082 GGT-CTTTAGGGAAAATTTTATGT
1 GGTCCTTT-GGGAAAATTCTATGT
*
690105 GG-CACTTTGATGAAAATTCTATGT
1 GGTC-CTTTG-GGAAAATTCTATGT
690129 GG
1 GG
690131 CACTTCGGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
22 4 0.06
23 40 0.65
24 18 0.29
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
GGTCCTTTGGGAAAATTCTATGT
Found at i:690145 original size:24 final size:24
Alignment explanation
Indices: 690092--690151 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
690082 GGTCTTTAGG
* *
690092 GAAAATTTTATGTGGCACTTTGAT
1 GAAAATTATATGTGGCACTTCGAT
* *
690116 GAAAATTCTATGTGGCACTTCGGT
1 GAAAATTATATGTGGCACTTCGAT
*
690140 GCAAATTATATG
1 GAAAATTATATG
690152 AGCAATGGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.37
Consensus pattern (24 bp):
GAAAATTATATGTGGCACTTCGAT
Found at i:690882 original size:14 final size:14
Alignment explanation
Indices: 690863--690902 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
690853 CCGTGACCAA
690863 AAATCCCTAAATCT
1 AAATCCCTAAATCT
*
690877 AAATCCCCCAAAATCT
1 AAAT--CCCTAAATCT
690893 AAATCCCTAA
1 AAATCCCTAA
690903 TTCCCAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.41
16 13 0.59
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATCCCTAAATCT
Found at i:703588 original size:2 final size:2
Alignment explanation
Indices: 703581--703614 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
703571 TGTGTAAATA
703581 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
703615 TTTCAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:704597 original size:21 final size:21
Alignment explanation
Indices: 704573--704613 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
704563 CGGTAAAAAT
*
704573 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
704594 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
704614 TTTAACAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:713171 original size:3 final size:3
Alignment explanation
Indices: 713163--713189 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
713153 TAAAAGATCT
713163 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
713190 GGGTGTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:713885 original size:21 final size:22
Alignment explanation
Indices: 713852--713900 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
713842 TTTTTACTTA
*
713852 TAATATTAAATTTTAT-ATTTT
1 TAATATTAAATTTAATGATTTT
* *
713873 TAATTTTATATTTAATGATTTTT
1 TAATATTAAATTTAATGA-TTTT
713896 TAATA
1 TAATA
713901 ATTTTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 13 0.59
22 1 0.05
23 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TAATATTAAATTTAATGATTTT
Found at i:716739 original size:3 final size:3
Alignment explanation
Indices: 716733--716796 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
716723 ATAATAATAA
* * *
716733 ATT ATT ATT AAT ATT ACT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
716781 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
716797 CATTCACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:717729 original size:2 final size:2
Alignment explanation
Indices: 717724--717756 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
717714 TATTTTTTAT
*
717724 TA TA TA AA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
717757 ATGGATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:724616 original size:37 final size:37
Alignment explanation
Indices: 724510--724620 Score: 125
Period size: 38 Copynumber: 2.9 Consensus size: 37
724500 TTTGATGTTG
* * * *
724510 TTTCTCTTGAAACAAAGTGTCGTCTCGCTAGAGACATT
1 TTTCTCTTAAAACAAA-TTTCGTCTCGCTTGAGACAAT
*
724548 TTTTTCTTAAAAACAAATGTT-GTCTCGCTTGAGACAAT
1 TTTCTCTT-AAAACAAAT-TTCGTCTCGCTTGAGACAAT
* *
724586 TTTCTCTTAAAACAAATTTCATCTCACTTGAGACA
1 TTTCTCTTAAAACAAATTTCGTCTCGCTTGAGACA
724621 TATTCCATCA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
36 2 0.03
37 22 0.35
38 30 0.48
39 8 0.13
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (37 bp):
TTTCTCTTAAAACAAATTTCGTCTCGCTTGAGACAAT
Found at i:724926 original size:67 final size:67
Alignment explanation
Indices: 724814--724947 Score: 171
Period size: 67 Copynumber: 2.0 Consensus size: 67
724804 GTCTCTAACC
* * **
724814 TTTGAGATTGTTTACCTTGAAACAAAATTTCGTCTCTCTTTAGACAGTTTCTCTTGAAACATCCA
1 TTTGAGATCGTTTACCTTGAAACAAAATTTCGTCTCTCTTGAGACAACTTCTCTTGAAACAT-CA
724879 TCT
65 TCT
* * ** *
724882 TTTGAGATCGTTTCCCTTGAAAC-GAATTTTTTCTCTCTTGAGACAACTTCTCTTGAAGCATCAT
1 TTTGAGATCGTTTACCTTGAAACAAAATTTCGTCTCTCTTGAGACAACTTCTCTTGAAACATCAT
724946 CT
66 CT
724948 ATGAGTCAGT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 5 0.09
67 31 0.54
68 21 0.37
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.41
Consensus pattern (67 bp):
TTTGAGATCGTTTACCTTGAAACAAAATTTCGTCTCTCTTGAGACAACTTCTCTTGAAACATCAT
CT
Found at i:725307 original size:134 final size:132
Alignment explanation
Indices: 724974--725337 Score: 443
Period size: 134 Copynumber: 2.8 Consensus size: 132
724964 TGAAGCCATT
* * * * *
724974 ATCCCTAAAGATGGCCTGTCGTCCTCATCGCATAAGAACCA-TGCCATCCACCGACCAGACCTCC
1 ATCCCTAAAGATGGCCAGTCGTCCTCATCACGTAGGAACCAGTGTCATCCACCGACCAGACCTCC
* * * *
725038 TCATCACGTAGTAGCTGTGTCA-CCCTAGATAACCAGCTGTCCTCATCACGTAGGAACCATGTTA
66 TCATCAAGTAGGAGCCGTGTCACCCCTAGATAACCAGATGTCCTCATCACGTAGGAACCATGTTA
725102 TC
131 TC
* * *
725104 ATCCCTAAAGATGG-CATGTCGTCCTCATCATGTAGGAATC-GTGTCATCCACCGATCAGACCTC
1 ATCCCTAAAGATGGCCA-GTCGTCCTCATCACGTAGGAACCAGTGTCATCCACCGACCAGACCTC
* *
725167 CTCATCAAGTAGGAGCCGTGTCACCCCTAGATAACCAGATGTCCTCATCGCGTAGGAACCGTGTT
65 CTCATCAAGTAGGAGCCGTGTCACCCCTAGATAACCAGATGTCCTCATCACGTAGGAACCATGTT
725232 ATC
130 ATC
* * *
725235 A-CCCTTCCACAAGATGGCCAGCCGTCCTCATCACGTAGGAA-CAGTGTCATCCTCCGACCAGAT
1 ATCCC-T--A-AAGATGGCCAGTCGTCCTCATCACGTAGGAACCAGTGTCATCCACCGACCAGAC
* * * * *
725298 CTACTCATCATGTAGGAGGCGTGTCACCCTTAGACAACCA
62 CTCCTCATCAAGTAGGAGCCGTGTCACCCCTAGATAACCA
725338 TAACTCTTCA
Statistics
Matches: 201, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
129 1 0.00
130 75 0.37
131 43 0.21
133 2 0.01
134 78 0.39
135 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (132 bp):
ATCCCTAAAGATGGCCAGTCGTCCTCATCACGTAGGAACCAGTGTCATCCACCGACCAGACCTCC
TCATCAAGTAGGAGCCGTGTCACCCCTAGATAACCAGATGTCCTCATCACGTAGGAACCATGTTA
TC
Found at i:731669 original size:36 final size:36
Alignment explanation
Indices: 731629--731797 Score: 193
Period size: 36 Copynumber: 4.8 Consensus size: 36
731619 ATATTTACAA
* *
731629 TTATCAGAT-ATTTACAGTTATCAGATGATTTTTTAG
1 TTATCAGATGATTTACAATTATCAGATGA-TTTTCAG
* *
731665 TTATCAGAT-ATTTACAACTATTAGATGATTTTCAG
1 TTATCAGATGATTTACAATTATCAGATGATTTTCAG
*
731700 TTA-CTAGATGATTTTCAATTATCAGATGATTTTCAG
1 TTATC-AGATGATTTACAATTATCAGATGATTTTCAG
* * * * *
731736 TTATCATATGATTTTCAGTTATCAGAT-ATTTACAA
1 TTATCAGATGATTTACAATTATCAGATGATTTTCAG
*
731771 TTATTAGATGATTTACAATTATCAGAT
1 TTATCAGATGATTTACAATTATCAGAT
731798 AATTACAAAT
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
34 1 0.01
35 42 0.37
36 71 0.62
37 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (36 bp):
TTATCAGATGATTTACAATTATCAGATGATTTTCAG
Found at i:731695 original size:18 final size:18
Alignment explanation
Indices: 731621--731797 Score: 173
Period size: 18 Copynumber: 9.9 Consensus size: 18
731611 CAAGTATGAT
731621 ATTTACAATTATCAGAT-
1 ATTTACAATTATCAGATG
*
731638 ATTTACAGTTATCAGATG
1 ATTTACAATTATCAGATG
** *
731656 ATTTTTTAGTTATCAGAT-
1 A-TTTACAATTATCAGATG
* *
731674 ATTTACAACTATTAGATG
1 ATTTACAATTATCAGATG
* *
731692 ATTTTCAGTTA-CTAGATG
1 ATTTACAATTATC-AGATG
*
731710 ATTTTCAATTATCAGATG
1 ATTTACAATTATCAGATG
* * *
731728 ATTTTCAGTTATCATATG
1 ATTTACAATTATCAGATG
* *
731746 ATTTTCAGTTATCAGAT-
1 ATTTACAATTATCAGATG
*
731763 ATTTACAATTATTAGATG
1 ATTTACAATTATCAGATG
731781 ATTTACAATTATCAGAT
1 ATTTACAATTATCAGAT
731798 AATTACAAAT
Statistics
Matches: 134, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
17 41 0.31
18 78 0.58
19 15 0.11
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (18 bp):
ATTTACAATTATCAGATG
Found at i:731709 original size:54 final size:53
Alignment explanation
Indices: 731618--731797 Score: 213
Period size: 53 Copynumber: 3.4 Consensus size: 53
731608 GCCCAAGTAT
* * *
731618 GATATTTACAATTATCAGAT-ATTTACAGTTATCAGATGATTTTTTAGTTATCA
1 GATATTTACAATTATCAGATGATTTTCAGTTATCAGATGA-TTTTCAATTATCA
* *
731671 GATATTTACAACTATTAGATGATTTTCAGTTA-CTAGATGATTTTCAATTATCA
1 GATATTTACAATTATCAGATGATTTTCAGTTATC-AGATGATTTTCAATTATCA
* * * * *
731724 GATGATTTTCAGTTATCATATGATTTTCAGTTATCAGAT-ATTTACAATTATTA
1 GAT-ATTTACAATTATCAGATGATTTTCAGTTATCAGATGATTTTCAATTATCA
731777 GATGATTTACAATTATCAGAT
1 GAT-ATTTACAATTATCAGAT
731798 AATTACAAAT
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
53 63 0.58
54 44 0.41
55 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (53 bp):
GATATTTACAATTATCAGATGATTTTCAGTTATCAGATGATTTTCAATTATCA
Found at i:731777 original size:89 final size:91
Alignment explanation
Indices: 731616--731784 Score: 272
Period size: 89 Copynumber: 1.9 Consensus size: 91
731606 CTGCCCAAGT
*
731616 ATGATATTTACAATTATCAGATATTTACAGTTATCAGATGATTTTTTAGTTATCAGATATTTACA
1 ATGATATTTACAATTATCAGATATTTACAGTTATCAGATGATTTTTCAGTTATCAGATATTTACA
731681 ACTATTAGATGATTTTCAGTTACTAG
66 ACTATTAGATGATTTTCAGTTACTAG
* *
731707 ATGAT-TTT-CAATTATCAGATGATTTTCAGTTATCATATGA-TTTTCAGTTATCAGATATTTAC
1 ATGATATTTACAATTATCAGAT-ATTTACAGTTATCAGATGATTTTTCAGTTATCAGATATTTAC
*
731769 AATTATTAGATGATTT
65 AACTATTAGATGATTT
731785 ACAATTATCA
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
89 48 0.66
90 20 0.27
91 5 0.07
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (91 bp):
ATGATATTTACAATTATCAGATATTTACAGTTATCAGATGATTTTTCAGTTATCAGATATTTACA
ACTATTAGATGATTTTCAGTTACTAG
Found at i:736699 original size:17 final size:17
Alignment explanation
Indices: 736677--736711 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
736667 TAATTCCTGC
*
736677 ATCAAATTCATCTCTAA
1 ATCAAATGCATCTCTAA
736694 ATCAAATGCATCTCTAA
1 ATCAAATGCATCTCTAA
736711 A
1 A
736712 AAGGCTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.03, T:0.31
Consensus pattern (17 bp):
ATCAAATGCATCTCTAA
Found at i:737882 original size:7 final size:7
Alignment explanation
Indices: 737867--737909 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
737857 GAGATCTAAA
737867 ACCTGTC
1 ACCTGTC
*
737874 ACCTTTC
1 ACCTGTC
737881 ACCTGTC
1 ACCTGTC
*
737888 ACCTTTC
1 ACCTGTC
737895 ACCTGTC
1 ACCTGTC
737902 ACCTGTC
1 ACCTGTC
737909 A
1 A
737910 GTTGTTTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.16, C:0.42, G:0.09, T:0.33
Consensus pattern (7 bp):
ACCTGTC
Found at i:737886 original size:14 final size:14
Alignment explanation
Indices: 737867--737905 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
737857 GAGATCTAAA
737867 ACCTGTCACCTTTC
1 ACCTGTCACCTTTC
737881 ACCTGTCACCTTTC
1 ACCTGTCACCTTTC
737895 ACCTGTCACCT
1 ACCTGTCACCT
737906 GTCAGTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.15, C:0.44, G:0.08, T:0.33
Consensus pattern (14 bp):
ACCTGTCACCTTTC
Found at i:749721 original size:20 final size:20
Alignment explanation
Indices: 749696--749746 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
749686 CACTTAGGGA
749696 ACCGATTCCCCATAGGGGGT
1 ACCGATTCCCCATAGGGGGT
*
749716 ACCGATTCCCTATAGGGGGT
1 ACCGATTCCCCATAGGGGGT
749736 ACCGATTCCCC
1 ACCGATTCCCC
749747 CCACGCTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.22
Consensus pattern (20 bp):
ACCGATTCCCCATAGGGGGT
Found at i:754664 original size:21 final size:22
Alignment explanation
Indices: 754618--754709 Score: 66
Period size: 21 Copynumber: 4.2 Consensus size: 22
754608 ACGCCTAACA
* * *
754618 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGAT-CACACCATGAAG
*
754640 GTGCATCGAT-ATACCATGAAG
1 GTGCATCGATCACACCATGAAG
* * *
754661 GTGCA-CTGATGCACGCCTTGAAT
1 GTGCATC-GAT-CACACCATGAAG
754684 GTGCATCGAT-ACACCATGAAG
1 GTGCATCGATCACACCATGAAG
754705 GTGCA
1 GTGCA
754710 CCTAACAAGG
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
20 2 0.04
21 27 0.49
22 10 0.18
23 15 0.27
24 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATCACACCATGAAG
Found at i:757447 original size:65 final size:63
Alignment explanation
Indices: 757378--757535 Score: 194
Period size: 65 Copynumber: 2.5 Consensus size: 63
757368 ATAAATTGAT
* * *
757378 CATCGAATGCATTTCATGCACCGATGCACATACTATGCATCGATGCAGTCAGAG-T-TTTATGAA
1 CATCGAATGCATTTCATGCATCGATGCACA-ACCATGCATCGATGCAATCAG-GCTATTT-TG-A
757441 AA
62 AA
* *
757443 CATCGAATGCATTTGATACATCGATGCACCAACCATGCATCGATGCAATCAGGCTATTTTGAAA
1 CATCGAATGCATTTCATGCATCGATGCA-CAACCATGCATCGATGCAATCAGGCTATTTTGAAA
* *
757507 CATCGAATGCATTTTATGCATTGATGCAC
1 CATCGAATGCATTTCATGCATCGATGCAC
757536 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
63 1 0.01
64 29 0.35
65 47 0.57
66 5 0.06
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (63 bp):
CATCGAATGCATTTCATGCATCGATGCACAACCATGCATCGATGCAATCAGGCTATTTTGAAA
Found at i:776110 original size:42 final size:41
Alignment explanation
Indices: 776051--776129 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
776041 CCATCAGTAT
* *
776051 GTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA
1 GTCTTTCGAGCAAGATGA-TAAATCCTTCGGGCCATCTGTCA
*
776093 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCT
1 GTCTTTCGAGCAAGATGATAAATCCTTCGGGCCATCT
776130 ATAAGACGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 17 0.50
42 17 0.50
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (41 bp):
GTCTTTCGAGCAAGATGATAAATCCTTCGGGCCATCTGTCA
Found at i:777080 original size:44 final size:43
Alignment explanation
Indices: 777011--777226 Score: 270
Period size: 44 Copynumber: 4.9 Consensus size: 43
777001 TGAGTGGAAC
* **
777011 CTTTCTGCCAATAATACATTGTTATGCATTTTCATTTATGGCA
1 CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCA
* *
777054 TCTTTCTGCCAATAATGCACCTTTATGCATTTTTCATTTATGACA
1 -CTTTCTGCCAATAATGCACCGTTATGCA-TTTTCATTTATGGCA
**
777099 CAATCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCA
1 CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCA
* *
777142 CATTTATGCCAATAATGCACCGTTATGCATTTTCATTTGTGGCA
1 C-TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCA
* * ** *
777186 CATTTCTACTAATAATGCGTCGTTATACATTTTCATTTATG
1 C-TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATG
777227 AAATTATATT
Statistics
Matches: 150, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
43 15 0.10
44 121 0.81
45 14 0.09
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (43 bp):
CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCA
Found at i:781987 original size:20 final size:20
Alignment explanation
Indices: 781962--782012 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
781952 TAATATGAGC
781962 GTATCGGTACATTCAACTAT
1 GTATCGGTACATTCAACTAT
* **
781982 GTATCGATACATTCGGCTAT
1 GTATCGGTACATTCAACTAT
782002 GTATCGGTACA
1 GTATCGGTACA
782013 CTAATTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
GTATCGGTACATTCAACTAT
Found at i:786335 original size:44 final size:44
Alignment explanation
Indices: 786279--786677 Score: 546
Period size: 44 Copynumber: 9.0 Consensus size: 44
786269 AAACTATGAG
*** * *
786279 TGGCACCTTTCTGCCAATAATGCATTTTTAGGTATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
786323 TGGTATCTTTCTGCCAATAATGCACCTTTATGCATTTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCA-TTTTCATTTA
*
786368 TGGCACCTTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
786412 TGACACCTTTCTGCCAATAATGCACCGTTATACATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
786456 TGGCACCTTTTTGCTAATAATGCAACGTTATACATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* **
786500 TGGAACCTTTCTGCCAATAATGCACTATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
786544 TGGCACCTTTCTTCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
786588 TGGCACATTTATGCCAATAATGCAACGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * **
786632 TGGTACATTTCTTCCAATAATGCACTATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
786676 TG
1 TG
786678 AAATTATATT
Statistics
Matches: 316, Mismatches: 38, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
44 276 0.87
45 40 0.13
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:788140 original size:42 final size:41
Alignment explanation
Indices: 788079--788167 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 41
788069 AATTGGTAAG
* * *
788079 TCCTTCGGGCCATTAGTAAGTTTTTCGAGCATGATGATTAAA
1 TCCTTCAGGCCATTAGTAAGTCTTTCGAGCAAGATGA-TAAA
* * *
788121 TCCTTCAGGTCATTTGTAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCAGGCCATTAGTAAGTCTTTCGAGCAAGATGATAAA
788162 TCCTTC
1 TCCTTC
788168 GAGCCATCCG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 9 0.22
42 32 0.78
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (41 bp):
TCCTTCAGGCCATTAGTAAGTCTTTCGAGCAAGATGATAAA
Found at i:788531 original size:3 final size:3
Alignment explanation
Indices: 788523--788563 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
788513 TTTTGTCCAG
788523 ATT ATT ATTT ATT ATT ATT ATT ATT -TAT ATT ATT ATT ATT A
1 ATT ATT A-TT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A
788564 ATTTTTGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 30 0.86
4 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:793489 original size:39 final size:41
Alignment explanation
Indices: 793446--793533 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
793436 GTTTATAATC
793446 CAAACGCCAC-A-AAACGA-TACTTTAGCGGCGATTCTTAAA
1 CAAACGCCACTATAAACGAGTACTTTAGCGGCG-TTCTTAAA
* ** * *
793485 CAAACGCCGCTATAAATTAGTACTTTAGCGGCGTTTTTATA
1 CAAACGCCACTATAAACGAGTACTTTAGCGGCGTTCTTAAA
793526 CAAACGCC
1 CAAACGCC
793534 GCAATAGAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 9 0.22
40 1 0.02
41 18 0.44
42 13 0.32
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (41 bp):
CAAACGCCACTATAAACGAGTACTTTAGCGGCGTTCTTAAA
Found at i:793572 original size:83 final size:83
Alignment explanation
Indices: 793483--793705 Score: 295
Period size: 83 Copynumber: 2.7 Consensus size: 83
793473 GCGATTCTTA
* *
793483 AACAAACGCCGCTATAAATTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGATCGT
1 AACAAACGCCGCAATAAATTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATAGAGATCGT
* * *
793548 TTATAGTGGCGTTTTTCT
66 TCATAGTGGCATTTTTCC
* * * * * * *
793566 AACAAACGCCGCGATAGATTAGTACTTTAGCAGTGTTTTTATACAAACGTCGCAATAGGGTTTGT
1 AACAAACGCCGCAATAAATTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATAGAGATCGT
793631 TCATAGTGGCATTTTTCC
66 TCATAGTGGCATTTTTCC
* * * *
793649 AACAAACGTCGCAATAAA-GAGTACTTTAGTAGCGTTTTTATATAAACGCCGCAATAG
1 AACAAACGCCGCAATAAATTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATAG
793706 GGTTCTTTAT
Statistics
Matches: 121, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
82 34 0.28
83 87 0.72
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (83 bp):
AACAAACGCCGCAATAAATTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATAGAGATCGT
TCATAGTGGCATTTTTCC
Found at i:793604 original size:42 final size:41
Alignment explanation
Indices: 793463--793907 Score: 182
Period size: 41 Copynumber: 10.9 Consensus size: 41
793453 CACAAAACGA
* * * *
793463 TACTTTAGCGGCGATTCTTAAACAAACGCCGCTATAAATTAG
1 TACTTTAGCGGCG-TTTTTATACAAACGCCGCAATAGATTAG
* *
793505 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGATCG
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGA-TTAG
* * *
793547 T--TTATAGTGGCGTTTTTCTAACAAACGCCGCGATAGATTAG
1 TACTT-TAGCGGCGTTTTTAT-ACAAACGCCGCAATAGATTAG
* * * * *
793588 TACTTTAGCAGTGTTTTTATACAAACGTCGCAATAGGGTTTG
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATA-GATTAG
* * * * * **
793630 TTC-ATAGTGGCATTTTTCCA-ACAAACGTCGCAATA-AAGAG
1 TACTTTAGCGGCGTTTTT--ATACAAACGCCGCAATAGATTAG
** * *
793670 TACTTTAGTAGCGTTTTTATATAAACGCCGCAATAG---GG
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGATTAG
* * ** * * * * * * *
793708 TTCTTTATCTACGTTTATGCA-AAAAATGTCGCGA-CGACGTAG
1 TACTTTAGCGGCGTTT-T-TATACAAACGCCGCAATAGA-TTAG
* * * *
793750 TACTTTAGCGGCGTTTTTCTACAAATGCCGCAATAAATCAG
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGATTAG
* * *
793791 TGA-ATTAGCAGCGTTTTTAAATACAAACGCCACAA-A-A-TAG
1 T-ACTTTAGCGGCGTTTTT--ATACAAACGCCGCAATAGATTAG
* * * * **
793831 TAACATTAGCGGCGTTTTT-TAAAAAACGCCGCAAGAAATCGG
1 T-ACTTTAGCGGCGTTTTTAT-ACAAACGCCGCAATAGATTAG
* * *
793873 TCCATTAGCGGCGTTTTTAAACAAACGCCGCAATA
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATA
793908 AGTTAGTGAA
Statistics
Matches: 298, Mismatches: 77, Indels: 57
0.69 0.18 0.13
Matches are distributed among these distances:
38 14 0.05
39 22 0.07
40 24 0.08
41 141 0.47
42 82 0.28
43 15 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGATTAG
Found at i:793799 original size:41 final size:41
Alignment explanation
Indices: 793754--793947 Score: 162
Period size: 41 Copynumber: 4.7 Consensus size: 41
793744 ACGTAGTACT
* *
793754 TTAGCGGCGTTTTTCTACAAATGCCGCAATAAATCAGTGAA
1 TTAGCGGCGTTTTTATACAAACGCCGCAATAAATCAGTGAA
* * *
793795 TTAGCAGCGTTTTTAAATACAAACGCCAC-A-AAAT-AGTAACA
1 TTAGCGGCGTTTTT--ATACAAACGCCGCAATAAATCAGTGA-A
* * * **
793836 TTAGCGGCGTTTTT-TAAAAAACGCCGCAAGAAATCGGTCCA
1 TTAGCGGCGTTTTTAT-ACAAACGCCGCAATAAATCAGTGAA
* * *
793877 TTAGCGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTGAA
1 TTAGCGGCGTTTTTATACAAACGCCGCAATAAATCAGTGAA
* * * *
793918 GTAGTGGCGTTTTAAATACAAACGCTGCAA
1 TTAGCGGCGTTTT-TATACAAACGCCGCAA
793948 GTTTTGGATA
Statistics
Matches: 120, Mismatches: 24, Indels: 17
0.75 0.15 0.11
Matches are distributed among these distances:
38 1 0.01
39 9 0.08
40 5 0.04
41 79 0.66
42 16 0.13
43 10 0.08
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (41 bp):
TTAGCGGCGTTTTTATACAAACGCCGCAATAAATCAGTGAA
Found at i:798060 original size:86 final size:83
Alignment explanation
Indices: 797970--798238 Score: 225
Period size: 86 Copynumber: 3.1 Consensus size: 83
797960 ATAACATGTA
* * * *
797970 GCGGCATTTTCGATAAAAACGCCGCAAAATCTCAACGCTTATTGCGGCGCTTGTTTGAAAAACGC
1 GCGGCATTTTTGAGAAAAACGCCGCTAAA--TCAACGCCTATTGCGGCG-TTGTTTGAAAAACGC
798035 CGCTAAACAACAACACCTATT
63 CGCTAAACAACAACACCTATT
* * * ***
798056 GCGGCCTTTTTGGGAAAAACGCCGCTAAA-CAACGATACCTACTGCGGCGTTTGGGGGAAAAACG
1 GCGGCATTTTTGAGAAAAACGCCGCTAAATCAACG---CCTATTGCGGCG-TTGTTTGAAAAACG
* *
798120 CCGCTAAACGACAACACTTATT
62 CCGCTAAACAACAACACCTATT
* * * * * *
798142 ACGGCATTTTTAAGACAAACGCCGCTAAATAGCAACACCTATTGCGGCGTTTTTTCAACAAACGC
1 GCGGCATTTTTGAGAAAAACGCCGCTAAAT--CAACGCCTATTGCGGCGTTGTTTGAA-AAACGC
* * * **
798207 CGCTATATATCGTCACCTATT
63 CGCTAAACAACAACACCTATT
*
798228 GCGGCGTTTTT
1 GCGGCATTTTT
798239 CATTAACAAA
Statistics
Matches: 142, Mismatches: 34, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
83 5 0.04
85 4 0.03
86 129 0.91
89 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (83 bp):
GCGGCATTTTTGAGAAAAACGCCGCTAAATCAACGCCTATTGCGGCGTTGTTTGAAAAACGCCGC
TAAACAACAACACCTATT
Found at i:798210 original size:43 final size:42
Alignment explanation
Indices: 797984--798238 Score: 204
Period size: 43 Copynumber: 6.0 Consensus size: 42
797974 CATTTTCGAT
* ** * * *
797984 AAAAACGCCGCAAAATCTCAACGCTTATTGCGGCGCTTGTTTG
1 AAAAACGCCGCTAAATAACAACACCTATTGCGGCG-TTTTTTG
* * *
798027 AAAAACGCCGCTAAACAACAACACCTATTGCGGCCTTTTTGGG
1 AAAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTT-TG
* * * * ***
798070 AAAAACGCCGCTAAACAACGATACCTACTGCGGCGTTTGGGGG
1 AAAAACGCCGCTAAATAACAACACCTATTGCGGCGTTT-TTTG
** * * * *
798113 AAAAACGCCGCTAAACGACAACACTTATTACGGCATTTTTAAG
1 AAAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTT-TG
* * *
798156 ACAAACGCCGCTAAATAGCAACACCTATTGCGGCGTTTTTTC
1 AAAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTTG
* * **
798198 AACAAACGCCGCTATATATCGTCACCTATTGCGGCGTTTTT
1 AA-AAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTT
798239 CATTAACAAA
Statistics
Matches: 169, Mismatches: 39, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
42 5 0.03
43 164 0.97
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTTG
Found at i:800657 original size:8 final size:8
Alignment explanation
Indices: 800644--800697 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
800634 AATTATTAGT
800644 TATAATAA
1 TATAATAA
800652 TATAATATAA
1 TAT-A-ATAA
800662 TATAATAA
1 TATAATAA
800670 TA-ATATAA
1 TATA-ATAA
800678 T-T-ATAA
1 TATAATAA
*
800684 TATAATTA
1 TATAATAA
800692 TATAAT
1 TATAAT
800698 TATAGTGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
6 5 0.13
7 2 0.05
8 23 0.59
9 2 0.05
10 7 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TATAATAA
Found at i:800658 original size:5 final size:5
Alignment explanation
Indices: 800648--800697 Score: 68
Period size: 5 Copynumber: 10.0 Consensus size: 5
800638 ATTAGTTATA
800648 ATAAT ATAAT ATAAT ATAAT AATAAT ATAATT ATAAT ATAAT -T-AT ATAAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT
800698 TATAGTGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 27 0.66
6 10 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:800690 original size:11 final size:11
Alignment explanation
Indices: 800648--800693 Score: 76
Period size: 11 Copynumber: 4.3 Consensus size: 11
800638 ATTAGTTATA
800648 ATAATATAA-T
1 ATAATATAATT
*
800658 ATAATATAATA
1 ATAATATAATT
800669 ATAATATAATT
1 ATAATATAATT
800680 ATAATATAATT
1 ATAATATAATT
800691 ATA
1 ATA
800694 TAATTATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAATATAATT
Found at i:801018 original size:43 final size:43
Alignment explanation
Indices: 800958--801105 Score: 133
Period size: 43 Copynumber: 3.4 Consensus size: 43
800948 CTTAAAAAGA
*
800958 ATTTGGTT-CACTACTCTTCCATGAAGATTAGATTCAAAGTTG
1 ATTTGCTTCCACTACTCTTCCATGAAGATTAGATTCAAAGTTG
* * * *
801000 ATTTGCCTCCACTACTCTTCCATGGAGATTGGATAGACTTGAAAG--A
1 ATTTGCTTCCACTACTCTTCCATGAAGA-T---TAGA-TTCAAAGTTG
* * * * *
801046 ATATG-TTTCACTACTCTTCCGTGAAGATCAGATTCAATGTTG
1 ATTTGCTTCCACTACTCTTCCATGAAGATTAGATTCAAAGTTG
801088 ATTTGCTTCCACTACTCT
1 ATTTGCTTCCACTACTCT
801106 CCCGTAGAGA
Statistics
Matches: 81, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
40 5 0.06
41 3 0.04
42 10 0.12
43 29 0.36
44 2 0.02
45 18 0.22
46 4 0.05
47 4 0.05
48 6 0.07
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (43 bp):
ATTTGCTTCCACTACTCTTCCATGAAGATTAGATTCAAAGTTG
Found at i:805554 original size:20 final size:20
Alignment explanation
Indices: 805517--805555 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
805507 AGATTGAGTG
* * *
805517 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
805537 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
805556 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:805783 original size:20 final size:21
Alignment explanation
Indices: 805737--805797 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
805727 TTCCCCTGTG
805737 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
805760 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
805780 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
805798 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:818817 original size:22 final size:22
Alignment explanation
Indices: 818789--818833 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
818779 CAATAGGGAG
818789 TTGATTT-TCCTTTCTCTGATGA
1 TTGATTTGT-CTTTCTCTGATGA
818811 TTGATTTGTCTTTCTCTGATGA
1 TTGATTTGTCTTTCTCTGATGA
818833 T
1 T
818834 CCTGAACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.13, C:0.16, G:0.16, T:0.56
Consensus pattern (22 bp):
TTGATTTGTCTTTCTCTGATGA
Found at i:820803 original size:16 final size:16
Alignment explanation
Indices: 820782--820825 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
820772 ACGAACCTAA
820782 CCGCATGATTTCTAGT
1 CCGCATGATTTCTAGT
820798 CCGCATGATTTCTAGT
1 CCGCATGATTTCTAGT
*
820814 TCGCATGCATTT
1 CCGCATG-ATTT
820826 AAAAAAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (16 bp):
CCGCATGATTTCTAGT
Found at i:823545 original size:5 final size:5
Alignment explanation
Indices: 823186--823538 Score: 577
Period size: 5 Copynumber: 72.2 Consensus size: 5
823176 ATTAGTTATA
823186 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-AAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
823235 AT-AT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
823282 ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
823331 ATAAT AT-AT ATAAT ATAATAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
823382 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
823430 ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
823477 AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AATAAC ATAATT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAA-T
823528 ATAAT ATAAT A
1 ATAAT ATAAT A
823539 ATATAATTAT
Statistics
Matches: 330, Mismatches: 2, Indels: 32
0.91 0.01 0.09
Matches are distributed among these distances:
3 6 0.02
4 30 0.09
5 280 0.85
6 10 0.03
7 4 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:823699 original size:14 final size:15
Alignment explanation
Indices: 823671--823701 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
823661 AAATAAAGCA
823671 TATATTAAGAAAAAT
1 TATATTAAGAAAAAT
823686 TATATTAA-AAAAAT
1 TATATTAAGAAAAAT
823700 TA
1 TA
823702 GAACTTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
TATATTAAGAAAAAT
Found at i:824011 original size:31 final size:31
Alignment explanation
Indices: 823976--824050 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
823966 TAGGTGGATT
*
823976 TGTCAGAAATTTATGACGGATCCACATATTC
1 TGTCACAAATTTATGACGGATCCACATATTC
* * *
824007 TGTCACAAATTTGTGATGGGTCCACATATTC
1 TGTCACAAATTTATGACGGATCCACATATTC
**
824038 CATCACAAATTTA
1 TGTCACAAATTTA
824051 AATACTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (31 bp):
TGTCACAAATTTATGACGGATCCACATATTC
Found at i:837081 original size:15 final size:16
Alignment explanation
Indices: 837049--837082 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
837039 ATAATGTCCT
837049 AGATAGAGAACGAGTG
1 AGATAGAGAACGAGTG
*
837065 AGATAGA-AACTAGTG
1 AGATAGAGAACGAGTG
837080 AGA
1 AGA
837083 GGATAAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.47, C:0.06, G:0.32, T:0.15
Consensus pattern (16 bp):
AGATAGAGAACGAGTG
Found at i:837974 original size:23 final size:22
Alignment explanation
Indices: 837948--838011 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
837938 CAGCTCATAT
837948 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
837971 AATTGCACCGGAGTGTCACGTAG
1 AATTGCACC-TAGTGCCACGTAG
837994 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
838012 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:838152 original size:103 final size:103
Alignment explanation
Indices: 838019--838244 Score: 400
Period size: 103 Copynumber: 2.2 Consensus size: 103
838009 CCATATAATA
*
838019 ATGT-CCATAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
838083 GTCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
838122 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
*
838187 TTTCACCAGACCTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
* *
838225 ATGCCCCGAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
838245 GACCCTCTAC
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 115 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
Found at i:838760 original size:19 final size:20
Alignment explanation
Indices: 838723--838760 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
838713 CTTTTTATTA
*
838723 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
838743 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
838761 TATAGCATTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:849628 original size:11 final size:11
Alignment explanation
Indices: 849614--849639 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
849604 AACTCTAAGA
849614 TAACATGTTTC
1 TAACATGTTTC
849625 TAACATGTTTC
1 TAACATGTTTC
849636 TAAC
1 TAAC
849640 TTGTCCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (11 bp):
TAACATGTTTC
Done.